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Open Access Highly Accessed Research article

Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity

Luke J Mappley12*, Michael L Black23, Manal AbuOun1, Alistair C Darby4, Martin J Woodward2, Julian Parkhill5, A Keith Turner56, Matthew I Bellgard2, Tom La7, Nyree D Phillips7, Roberto M La Ragione18 and David J Hampson28

Author Affiliations

1 Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Reading University, Addlestone, Surrey, KT15 3NB, UK

2 Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire, RG6 6AP, UK

3 School of Medical Sciences, Edith Cowan University, Perth, WA, 6027, Australia

4 Institute of Integrative Biology, School of Biological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK

5 The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

6 Discuva Ltd, Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK

7 School of Veterinary and Biomedical Science, Murdoch University, Perth, WA, 6150, Australia

8 Faculty of Health and Medical Sciences, University of Surrey, Guilford, Surrey, GU2 7XH, UK

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BMC Genomics 2012, 13:454  doi:10.1186/1471-2164-13-454

Published: 5 September 2012

Abstract

Background

The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a porcine isolate. In the first intra-species genome comparison within the Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on incomplete genome sequences from three other Brachyspira species. Finally we report the first application of the high-throughput Biolog phenotype screening tool on the B. pilosicoli strains for detailed comparisons between genotype and phenotype.

Results

Feature and sequence genome comparisons revealed a high degree of similarity between the three B. pilosicoli strains, although the genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and 2.596 Mb, respectively). Genome rearrangements were observed which correlated largely with the positions of mobile genetic elements. Through comparison of the B2904 and WesB genomes with the 95/1000 genome, features that we propose are non-essential due to their absence from 95/1000 include a peptidase, glycine reductase complex components and transposases. Novel bacteriophages were detected in the newly-sequenced genomes, which appeared to have involvement in intra- and inter-species horizontal gene transfer. Phenotypic differences predicted from genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000, were confirmed by phenotyping.

Conclusions

The availability of multiple B. pilosicoli genome sequences has allowed us to demonstrate the substantial genomic variation that exists between these strains, and provides an insight into genetic events that are shaping the species. In addition, phenotype screening allowed determination of how genotypic differences translated to phenotype. Further application of such comparisons will improve understanding of the metabolic capabilities of Brachyspira species.

Keywords:
Brachyspira pilosicoli; Spirochaete; Colitis; Zoonosis; Whole genome sequencing; Genome comparison; Horizontal gene transfer; Phenotype MicroArrayâ„¢